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Identification of putative genetic regions for watermelon rind hardness and related traits by BSA-seq and QTL mapping

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Abstract

Textural quality of watermelon fruit is mainly determined by rind hardness/firmness and its related traits. The determination of genetic regions harboring QTLs/gene(s) has a primary worth in genetic breeding studies. In this study, whole genome BSA-seq and QTL mapping through newly developed CAPS markers were successfully performed, respectively. Total 133-F2 mapping individuals were derived from crossing of P1 ‘1061’ and P2 ‘812’ and slefing of F1 offspring. Whole genome BSA-seq revealed major genetic region controlling rind hardness trait on chromosome 10. The genetic linkage map was assembled by genotyping of 133 pairs of codominant CAPS markers which spanned total 2606.38 cM length with averaged 19.60 cM distance among whole genome flanking markers. Moreover, CAPS markers based QTL analysis revealed total 5 putative QTLs [2 rind-hardness (RH), 1 rind toughness (RTO), 1 rind thickness (RTH) and 1 fruit weight (FW)] on three distinct chromosomes (2, 9, and 10), which mainly contributed 5.44–49.11% PVE. Interestingly, the combined molecular techniques expressed putative genetic region controlling rind hardness at chromosome 10. According to the BSA-seq result, major genetic region was detected between 1792001 and 4036000 bp on chromosome 10 with 2.24 Mb range, while from QTLs analysis, two co-localized focal QTLs “RH10 and RTO10” revealed 20 and 39 predicted genes at shortened genetic distances of 292.76 kbp and 405.31 kbp, respectively. A significant correlation and normal distribution frequencies for rind-phenotypes were also noticed. In crux, our combined techniques proved as an effective mapping strategies for identification of QTLs/gene(s) and provided a strong theoretical basis for future breeding studies in watermelon.

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Acknowledgements

All authors are thankful for financial funding supported by 538-National Key Research and Development Program (2018YFD0100703) , 539-China Agriculture Research System (CARS-25), and National Nature Science Foundation of China (Project No. 31772333). Authors are also grateful to Chinese Academy of Agricultural Sciences, Zhengzhou Fruit Research Institute, Henan, for provision of experimental resources.

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  1. College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, Heilongjiang, People’s Republic of China

    Tiantian Yang, Sikandar Amanullah, Jiahui Pan, Guixiang Chen, Shi Liu, Peng Gao & Xuezheng Wang

  2. Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, People’s Republic of China

    Tiantian Yang, Sikandar Amanullah, Jiahui Pan, Guixiang Chen, Shi Liu, Peng Gao & Xuezheng Wang

  3. Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, Henan Province, People’s Republic of China

    Shuangwu Ma & Jiming Wang

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  1. Tiantian Yang
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Yang, T., Amanullah, S., Pan, J. et al. Identification of putative genetic regions for watermelon rind hardness and related traits by BSA-seq and QTL mapping. Euphytica 217, 19 (2021). https://doi.org/10.1007/s10681-020-02758-9

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